How to Find Information about a Gene of Interest?

“Gene of Interest (GOI) is a target for various genetic studies. Learn about how you can find various information about GOI in this article.” 

Gene is the basic unit of inheritance present on these chromosomes at a specific position known as a locus. Some genes encode proteins which are necessary for carrying out various processes in the body. The human genome contains around 20,000 protein-coding genes. Genes are passed on from parents to offspring.

Genes are studied to find mutations, alterations, gene expression, and disease associated. However, to study a gene we need several pre-research information. Some such information includes gene location, sequence, length, exons, and several pathogenic and non-pathogenic mutations. 

This information is already available online on various platforms. Many of them are freely available but students lack the complete knowledge of how to find and process such information. 

No look further. 

In this article, I will explain to you a step-by-step process using which you can find information regarding any gene. But before that, we will learn what GOI is and why we study it. 

We are dividing this article into two parts and using two separate databases to understand the present topic. First, we will discuss the NCBI (to find information on GOI) and second ClinVar (to find information on mutations). 

Stay tuned. 

Read more: The Human Genome Project: Aims, Objectives, Techniques and Outcomes.

What is GOI? 

GOI is Gene Of Interest, a specific term that refers to a gene or DNA sequence used for a genetic experiment. It can be used for a basic dissertation-level experiment to advanced gene editing-level research. 

Put simply, GOI is a target DNA sequence or gene on which a researcher or scientist is going to conduct their research. For instance, for mutational mapping of the BRCA1 gene, our gene of interest is BRCA1. Now we use various techniques to study and find out the mutations present in the gene. 

So GOI is used for 

• Functional and structural characterization of a gene. 
• Identify disease-causing variants associated with a gene. 
• Identify and map various mutations present in a gene. 
• Drug and marker development.  

Now, imagine you want to conduct a research project on breast cancer and for what you want to study the BRCA1 gene. First, you need some basic and sequence-related information for the BRCA1 gene, now, how can you find it? 

Read more: Breast Cancer Genetics- Genes, Mutations, Inheritance, Testing and Diagnosis.

How to Find Information About a Gene of Interest? 

Let’s see the step-by-step by using the example of the BRCA1 gene and database NCBI. 

Step 1: Open Google, and enter NCBI in the search box. 

NCBI stands for National Center for Biotechnology Information. It is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It was founded in the year 1988 and is approved and funded by the government of the United States. The NCBI is a house to a series of databases relevant to both the basic and applied life sciences and is considered an important resource for bioinformatics tools and services.

Step 2: Once you have clicked on NCBI, the window of the NCBI site opens. 

Now, in the “search box” enter the name of the gene e.g. BRCA1 whose information you wish to collect. 

Besides the search box, there is a tab showing all databases, click on that tab and select “Gene” from the dropdown menu.

Step 3: Once you have selected Gene from the dropdown menu, click on the “search” button. 

This will open the page containing the list of all the genes related to BRCA1 present in all species. You can select a specific organism from the Top Organisms list present on the right-hand side of the page.  

Step 4: Once you select the species from the Top organisms, genes will be shown of only that particular species. E.g. Here I have selected Homo sapiens, so all the genes related to BRCA1 in Homo sapiens would only be displayed.

Step 5: Select the gene of your interest from the list. 

Once done, the page containing gene information will be displayed. This will showcase the official gene symbol, the full name of the gene, gene type, organism, lineage, and a summary of the gene.

Step 6: As you scroll down through the page, other information related to genes can be obtained such as Location and exon count.

The sequence of the gene can be retrieved in the form of a FASTA sequence. FASTA sequence always begins with the caret sign “>” followed by a unique SeqID and the nucleotide sequence.

Research papers related to the gene can be obtained through the Bibliography section.

This section will help you to navigate through various peer-reviewed resources that you can use for your research. 

Conditions associated with the gene can be found in the phenotype section.

Now coming to the second part of this tutorial. Suppose we want to study a particular clinical variant associated with the BRCA1 gene. How can we do that? Let’s find out. 

Note: Clinical variants are well-recognized and studied variants that have a role in disease development and progression. 

To learn about variants of the gene, click on See variants in ClinVar link in the Variation section.

Once clicked, you can select your desired variant by selecting appropriate filters present on the left-hand side of the page such as classification type, germline classification, type of conflicts, variation type, variation size, variation length, etc.

Suppose we want to study pathogenic deletion. Now what we will do is select,

• >> Germline from classification type 
• >> Pathogenic from germline classification
• >> Deletion from variation type 
• >> Short variant from variation size
• >> <1Kb from variation length

We will get a small list of deletions associated with a BRCA1 gene which are pathogenic. You can choose any one, two or many depending on your research scope and use for your research. 

Bonus:

From the gene information page, drop down more and click on “see SNP gene review report” to find information regarding the single nucleotide polymorphisms associated with the BRCA1 gene. 

What information will we get? 

For our example, we will get this information. 

Gene name	BRCA1
Full name	Breast Cancer Associated Gene 1
Location	17q21.31
Length	1,26,033 bp
Exon	31
FASTA format	Available
ClinVar	Germline pathogenic deletions <1Kb

In conclusion, you will get information regarding the gene’s official name, location, length, exons, FASTA format, gene bank and clinical variations. 

How to use this information? 

Now, you may have a question, how to use this information in your genetic experiment? No worries, we will also explain that as well. 

For instance, if you are doing a master’s level dissertation with limited scope and resources, you can choose any one pathogenic mutation (variant) such as deletion, duplication, translocation or simply SNP.

You can choose techniques like RFLP, conventional PCR or sequencing to analyze the variant from the patient samples. The FASTA format information will help you to design primers and restriction digestion experiments. 

Location and mapping information will help you validate the experiment in silico. The information regarding the exons and exons’ locations will help you know if the pathogenic variant is associated with any coding region or not. 

If your experiment is extensive, you can use this information to prepare your NGS experiment or design your costume microarray chip. 

The present information will further help you establish phenotype-genotype correlations and many more. 

Read more: What is Single Nucleotide Polymorphism (SNP)?- The Basics.

Wrapping up: 

In conclusion, the present “how-to” guide is a complete in silico analysis for your small large-scale research. To know more do check out the video tutorial. NCBI is a great place to explore your genetic knowledge and craft your research. 

In addition, further extensive information and tools are also present which certainly are not required for you right now. We will prepare tutorials on those tools and information later.

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